Main Figures
Figure 1
Sub-genomic RNA Expression is Increased in B.1.1.7 infections
## `summarise()` ungrouping output (override with `.groups` argument)
## # A tibble: 5 x 10
## orf .y. group1 group2 n1 n2 statistic p p.adj p.adj.signif
## <fct> <chr> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <chr>
## 1 S total B.1.1… B.1.1… 764 729 125745 3.84e-75 1.92e-74 ****
## 2 E total B.1.1… B.1.1… 764 729 217058 1.63e-13 4.89e-13 ****
## 3 M total B.1.1… B.1.1… 764 729 255940. 7.00e- 3 7.00e- 3 **
## 4 N total B.1.1… B.1.1… 764 729 127596 2.25e-73 9.00e-73 ****
## 5 ORF6 total B.1.1… B.1.1… 764 729 244833 5.34e- 5 1.07e- 4 ****
## # A tibble: 5 x 8
## .y. group1 group2 effsize orf n1 n2 magnitude
## * <chr> <chr> <chr> <dbl> <fct> <int> <int> <ord>
## 1 total B.1.177 B.1.1.7 0.475 S 764 729 moderate
## 2 total B.1.177 B.1.1.7 0.191 E 764 729 small
## 3 total B.1.177 B.1.1.7 0.0700 M 764 729 small
## 4 total B.1.177 B.1.1.7 0.469 N 764 729 moderate
## 5 total B.1.177 B.1.1.7 0.105 ORF6 764 729 small
## # A tibble: 5 x 10
## orf .y. group1 group2 n1 n2 statistic p p.adj p.adj.signif
## <fct> <chr> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <chr>
## 1 S total B.1.1… B.1.1… 179 150 5534. 4.18e-20 1.67e-19 ****
## 2 E total B.1.1… B.1.1… 179 150 11342. 1.50e- 2 1.60e- 2 *
## 3 M total B.1.1… B.1.1… 179 150 15702. 8.00e- 3 1.60e- 2 **
## 4 N total B.1.1… B.1.1… 179 150 4352 4.66e-26 2.33e-25 ****
## 5 ORF6 total B.1.1… B.1.1… 179 150 10121 1.21e- 4 3.63e- 4 ***
## # A tibble: 5 x 10
## orf .y. group1 group2 n1 n2 statistic p p.adj p.adj.signif
## <fct> <chr> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <chr>
## 1 S sgRN… B.1.1… B.1.1… 204 138 6900. 1.26e-15 6.30e-15 ****
## 2 E sgRN… B.1.1… B.1.1… 204 138 12444. 6.90e- 2 1.38e- 1 ns
## 3 M sgRN… B.1.1… B.1.1… 204 138 11952. 1.80e- 2 5.40e- 2 *
## 4 N sgRN… B.1.1… B.1.1… 204 138 7498. 2.25e-13 9.00e-13 ****
## 5 ORF6 sgRN… B.1.1… B.1.1… 204 138 13168. 3.11e- 1 3.11e- 1 ns
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
Figure 2
Relationship between day of symptom onset at sampling and sub-genomic RNA levels in B.1.1.7 and B.1.177 infections
## `summarise()` regrouping output by 'sample', 'lineage', 'Day_of_symptoms' (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
##
## Call:
## lm(formula = sgRPTg_HQ + sgRPTg_LQ ~ lineage + Day_of_symptoms,
## data = for_model_s)
##
## Residuals:
## Min 1Q Median 3Q Max
## -363.7 -98.9 -51.6 4.8 6370.6
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 67.795 32.832 2.065 0.0392 *
## lineageB.1.1 -5.401 38.010 -0.142 0.8870
## lineageB.1.1.7 295.879 37.450 7.901 7.64e-15 ***
## lineageB.1.177 50.925 36.341 1.401 0.1614
## Day_of_symptoms 6.480 3.582 1.809 0.0707 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 344.6 on 951 degrees of freedom
## Multiple R-squared: 0.1146, Adjusted R-squared: 0.1109
## F-statistic: 30.79 on 4 and 951 DF, p-value: < 2.2e-16
##
## Call:
## lm(formula = sgRPTg_HQ + sgRPTg_LQ ~ lineage + Day_of_symptoms,
## data = for_model_s)
##
## Residuals:
## Min 1Q Median 3Q Max
## -363.7 -98.9 -51.6 4.8 6370.6
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 67.795 32.832 2.065 0.0392 *
## lineageB.1.1 -5.401 38.010 -0.142 0.8870
## lineageB.1.1.7 295.879 37.450 7.901 7.64e-15 ***
## lineageB.1.177 50.925 36.341 1.401 0.1614
## Day_of_symptoms 6.480 3.582 1.809 0.0707 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 344.6 on 951 degrees of freedom
## Multiple R-squared: 0.1146, Adjusted R-squared: 0.1109
## F-statistic: 30.79 on 4 and 951 DF, p-value: < 2.2e-16
##
## Call:
## lm(formula = sgRPTg_HQ + sgRPTg_LQ ~ lineage + Day_of_symptoms,
## data = for_model_m)
##
## Residuals:
## Min 1Q Median 3Q Max
## -734.0 -269.0 -62.2 61.2 3270.4
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 78.083 46.293 1.687 0.092 .
## lineageB.1.1 35.578 53.593 0.664 0.507
## lineageB.1.1.7 605.706 52.803 11.471 <2e-16 ***
## lineageB.1.177 582.735 51.239 11.373 <2e-16 ***
## Day_of_symptoms 7.961 5.050 1.576 0.115
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 485.9 on 951 degrees of freedom
## Multiple R-squared: 0.2402, Adjusted R-squared: 0.237
## F-statistic: 75.16 on 4 and 951 DF, p-value: < 2.2e-16
##
## Call:
## lm(formula = sgRPTg_HQ + sgRPTg_LQ ~ lineage + Day_of_symptoms,
## data = for_model_n)
##
## Residuals:
## Min 1Q Median 3Q Max
## -473.9 -98.1 -37.5 44.1 12263.4
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 77.317 42.032 1.839 0.06616 .
## lineageB.1.1 40.524 48.661 0.833 0.40517
## lineageB.1.1.7 420.032 47.944 8.761 < 2e-16 ***
## lineageB.1.177 149.509 46.523 3.214 0.00135 **
## Day_of_symptoms 2.427 4.586 0.529 0.59680
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 441.1 on 951 degrees of freedom
## Multiple R-squared: 0.1173, Adjusted R-squared: 0.1136
## F-statistic: 31.6 on 4 and 951 DF, p-value: < 2.2e-16
##
## Call:
## lm(formula = sgRPTg_HQ + sgRPTg_LQ ~ lineage + Day_of_symptoms,
## data = for_model_orf6)
##
## Residuals:
## Min 1Q Median 3Q Max
## -276.4 -89.1 -54.0 -7.5 5705.6
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 77.566 29.817 2.601 0.00943 **
## lineageB.1.1 36.815 34.519 1.067 0.28646
## lineageB.1.1.7 -9.326 34.010 -0.274 0.78398
## lineageB.1.177 -10.737 33.003 -0.325 0.74501
## Day_of_symptoms 9.720 3.253 2.988 0.00288 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 312.9 on 951 degrees of freedom
## Multiple R-squared: 0.01596, Adjusted R-squared: 0.01182
## F-statistic: 3.856 on 4 and 951 DF, p-value: 0.004092
| S | E | M | N | ORF6 | |
|---|---|---|---|---|---|
| (Intercept) | 67.79 * | 67.79 * | 78.08 | 77.32 | 77.57 ** |
| (32.83) | (32.83) | (46.29) | (42.03) | (29.82) | |
| B.1.1 | -5.40 | -5.40 | 35.58 | 40.52 | 36.81 |
| (38.01) | (38.01) | (53.59) | (48.66) | (34.52) | |
| B.1.1.7 | 295.88 *** | 295.88 *** | 605.71 *** | 420.03 *** | -9.33 |
| (37.45) | (37.45) | (52.80) | (47.94) | (34.01) | |
| B.1.177 | 50.93 | 50.93 | 582.73 *** | 149.51 ** | -10.74 |
| (36.34) | (36.34) | (51.24) | (46.52) | (33.00) | |
| Days Since Symptom Onset | 6.48 | 6.48 | 7.96 | 2.43 | 9.72 ** |
| (3.58) | (3.58) | (5.05) | (4.59) | (3.25) | |
| N | 956 | 956 | 956 | 956 | 956 |
| R2 | 0.11 | 0.11 | 0.24 | 0.12 | 0.02 |
| *** p < 0.001; ** p < 0.01; * p < 0.05. | |||||
## Loading required namespace: broom.mixed
## Loading required namespace: broom.mixed
## Loading required namespace: broom.mixed
## Loading required namespace: broom.mixed
## Loading required namespace: broom.mixed
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Picking joint bandwidth of 0.895
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
Figure 3
A Non-canonical sgRNA representing ORF9b is highly expressed in B.1.1.7 due to a triple nucleotide mutation in nucleocapsid leading to the D3L substitution.
## `summarise()` regrouping output by 'start', 'y', 'lineage' (override with `.groups` argument)
## # A tibble: 1 x 7
## .y. group1 group2 effsize n1 n2 magnitude
## * <chr> <chr> <chr> <dbl> <int> <int> <ord>
## 1 total Other B.1.1.7 0.761 288 535 large